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Related Concept Videos

Protein Folding01:25

Protein Folding

7.8K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
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Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Conservation of Protein Domains02:26

Conservation of Protein Domains

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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Related Experiment Video

Updated: Jun 12, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Multistate and functional protein design using RoseTTAFold sequence space diffusion.

Sidney Lyayuga Lisanza1,2,3, Jacob Merle Gershon1,2,4, Samuel W K Tipps1,2

  • 1Department of Biochemistry, University of Washington, Seattle, WA, USA.

Nature Biotechnology
|September 25, 2024
PubMed
Summary
This summary is machine-generated.

ProteinGenerator (PG) is a new AI model that designs novel protein sequences and structures simultaneously. This advances protein design by enabling control over specific attributes and functions.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Area of Science:

  • Computational biology
  • Protein engineering
  • Artificial intelligence in life sciences

Background:

  • Protein denoising diffusion probabilistic models generate protein backbones but struggle with sequence-specific attributes and functions.
  • Existing models lack the ability to simultaneously generate protein sequences and their corresponding structures.

Purpose of the Study:

  • To develop an advanced protein design model capable of simultaneous sequence and structure generation.
  • To overcome limitations in guiding protein generation with specific sequence attributes and functional properties.

Main Methods:

  • Developed ProteinGenerator (PG), a sequence space diffusion model leveraging RoseTTAFold.
  • Employed iterative denoising from a noised sequence representation to generate sequence-structure pairs.
  • Guided generation using desired sequence and structural protein attributes.

Main Results:

  • Successfully designed thermostable proteins with tailored amino acid compositions and internal repeats.
  • Engineered cage structures for bioactive peptides like melittin.
  • Created multistate protein triples where a single sequence adopts different structures based on context.

Conclusions:

  • ProteinGenerator (PG) offers a powerful, generalizable approach for de novo protein design.
  • The model enables integrated computational and experimental optimization of protein function.
  • PG facilitates the design of proteins with complex structural and functional properties.